Dear galaxy users

Hello. I have a quick question about Cuffdiff analysis.
I have obtained two SRA files and converted them to fastq files which were
uploaded to Galaxy via FTP server. My analysis was followed by Fastq
groomer, Tophat, Cufflinks, Cuffcompare, and eventually Cuffdiff. (Gene
annotation was also downloaded from UCSC table browser in GTF format) I've
downloaded gene differential expression testing, one of the output files of
Cuffdiff, and viewed it in excel sheet. However, I have only zeros recorded
for value_1, value_2, log2, test_stat and only ones recorded for p_value
and q_value.

Is it likely that I might have obtained wrong gene annotation file and
caused this problem?

Thank you

Yona Kim
Department of Genetics
Rutgers University - New Brunswick Campus
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